A prototype version of The Revenge of Shinobi was bizarrely released by SEGA themselves. In 1999, SEGA Smash Pack was released for the PC in America. It includes several games, including The Revenge of Shinobi. However, somehow, a prototype version of the game was included instead of the final one. This prototype contains several differences from the final game, and isn't quite complete yet. For example, no ending sequence is in place, and certain boss fights are not ready yet. The game is also called "The Super Shinobi" no matter the region.

This proto also has a couple of cheats which never made it to the final. The first is a level select -activated by default, you can choose any level you want from the menu screen. In the options, there is also a "NO DEATH" option, which makes Joe invincible to almost everything, although you can still die by falling down bottomless pits.

The supercomputer boss doesn't work, and the sprites for it are all over the place. The laser cannons in the room are also missing, and the stage will just end itself after a few seconds. The boss fight against the dinosaur also isn't working correctly, as whilst the boss appears and moves around, it cannot hurt you, and you can't hurt it. Again, the stage will automatically end after a few seconds. There are also several graphical differences in this proto which are documented below: